/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
/*
* CytobandRenderer.java
*
* Created on September 19, 2007, 5:36 PM
*
* To change this template, choose Tools | Template Manager
* and open the template in the editor.
*/
package org.broad.igv.renderer;
import org.broad.igv.feature.Cytoband;
import org.broad.igv.ui.FontManager;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.panel.FrameManager;
import org.broad.igv.ui.panel.ReferenceFrame;
import java.awt.*;
import java.awt.geom.AffineTransform;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* @author jrobinso
*/
public class CytobandRenderer {
boolean drawLabels = true;
static final public int CYTOBAND_Y_OFFSET = 5;
static final public int LABEL_OFFSET = 25;
private static Map<Integer, Color> stainColors = new HashMap<Integer, Color>();
public void draw(List<Cytoband> data, Graphics g2D, Rectangle graphicRect, ReferenceFrame frame) {
if (data.size() > 0) {
// If we are in the process of exporting to an image file
// we need to write out the cytoband locus on the image
if (IGV.getInstance().isExportingSnapshot() || FrameManager.isGeneListMode()) {
String locus = frame.getChrName();
if (locus != null) {
Graphics g2 = g2D.create();
g2.setFont(FontManager.getFont(Font.BOLD, 11));
g2.drawString(locus, 3, 11);
g2.dispose();
}
}
// Draw Cytoband
drawBands(data, g2D, graphicRect, frame.getMaxCoordinate());
// Draw Cytoband Labels
if (drawLabels && !FrameManager.isGeneListMode()) {
drawLabels(g2D, graphicRect, data, frame.getMaxCoordinate());
}
}
}
public void drawBands(List<Cytoband> data, Graphics g2D, Rectangle graphicRect, int chromoLength) {
int[] xC = new int[3];
int[] yC = new int[3];
double scale = graphicRect.getWidth() / chromoLength;
int lastPX = -1;
for (Cytoband cytoband : data) {
int start = (int) (graphicRect.getX() + scale * cytoband.getStart());
int end = (int) (graphicRect.getX() + scale * cytoband.getEnd());
if (end > lastPX) {
int y = (int) graphicRect.getY() + CYTOBAND_Y_OFFSET;
int height = (int) graphicRect.getHeight();
if (cytoband.getType() == 'c') { // centermere: "acen"
int center = (y + height / 2);
if (cytoband.getName().startsWith("p")) {
xC[0] = start;
yC[0] = (int) graphicRect.getMaxY() + CYTOBAND_Y_OFFSET;
xC[1] = start;
yC[1] = y;
xC[2] = end;
yC[2] = center;
} else {
xC[0] = end;
yC[0] = (int) graphicRect.getMaxY() + CYTOBAND_Y_OFFSET;
xC[1] = end;
yC[1] = y;
xC[2] = start;
yC[2] = center;
}
g2D.setColor(Color.RED.darker());
g2D.fillPolygon(xC, yC, 3);
} else {
g2D.setColor(getCytobandColor(cytoband));
g2D.fillRect(start, y, (end - start), height);
g2D.setColor(Color.BLACK);
g2D.drawRect(start, y, (end - start), height);
}
}
lastPX = end;
}
}
private void drawLabels(final Graphics g, Rectangle graphicRect, List<Cytoband> cytobands, int chromoLength) {
double width = graphicRect.getWidth();
int y = (int) graphicRect.getY() + LABEL_OFFSET;
// Draw labels
g.setColor(Color.BLACK);
FontMetrics fm = g.getFontMetrics();
int minSpacing = 10;
int prevEnd = 0;
double sc = width / chromoLength;
int adjustedY = y;
if (cytobands != null) {
for (Cytoband cytoband : cytobands) {
int s = (int) (sc * cytoband.getStart());
int e = (int) (sc * cytoband.getEnd());
int stringWidth = (int) fm.getStringBounds(cytoband.getName(), g).getWidth();
int x = (int) (s + (e - s - stringWidth) / 2);
if (x > (prevEnd + minSpacing)) {
g.drawString(cytoband.getName(), x, adjustedY);
prevEnd = x + stringWidth;
}
}
}
}
public void applyTextTranslationAndRotation(Graphics2D graphics2, int x, int y) {
AffineTransform transform = new AffineTransform();
transform.translate(x, y);
transform.rotate(-Math.PI / 2);
graphics2.transform(transform);
}
private static Color getCytobandColor(Cytoband data) {
if (data.getType() == 'p') { // positive: "gpos100"
int stain = data.getStain(); // + 4;
int shade = (int) (255 - stain / 100.0 * 255);
Color c = stainColors.get(shade);
if (c == null) {
c = new Color(shade, shade, shade);
stainColors.put(shade, c);
}
return c;
} else if (data.getType() == 'c') { // centermere: "acen"
return Color.PINK;
} else {
return Color.WHITE;
}
}
}